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<h2 class="date-header"><span>Monday, June 29, 2009</span></h2>

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<h3 class="post-title entry-title">
Adding an extension for germplasm, GBIF IPT
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The <span style="font-weight: bold;">GBIF Provider Toolkit (IPT)</span> 
is a database wrapper to help the provider of biodiversity information 
to set up and provide these data as a web service. The primary data 
exchange standard deployed by the GBIF IPT is the <span style="font-weight: bold;">Darwin Core</span> standard maintained by the <b style="font-weight: normal;">Biodiversity Information Standards (</b>TDWG).<br>
<br>
<a href="http://code.google.com/p/gbif-providertoolkit/">http://code.google.com/p/gbif-providertoolkit/</a><br>
<a href="http://code.google.com/p/darwincore/">http://code.google.com/p/darwincore/</a><br>
<br>
Below are the steps I followed to develop a draft germplasm extension to
 the Darwin Core (DwC) standard, and next to add this draft DwC 
extension to the GBIF IPT software. You may follow the same steps to 
develop your own extension and to add this to the GBIF IPT.<br>
<br>
If you are interested, you may visit the IPT from NordGen with a DEMO 
dataset mapped to terms from this DRAFT Darwin Core extension for 
germplasm at:<br>
<a defaultcontextmenu="yes" href="http://ipt.nordgen.org/ipt/occResource.html?resource_id=77" target="_blank">http://ipt.nordgen.org/ipt/occResource.html?resource_id=77</a><br>
<br>
<span style="font-weight: bold;">Summary of steps:</span><br>
<br>
1. Schema<br>
I built a suggestion to a DRAFT Darwin Core extension for germplasm<br>
<a defaultcontextmenu="yes" href="http://code.google.com/p/darwincore/source/browse/trunk/xsd/profiles/germplasm/dwc_germplasm_0_1.xsd" target="_blank">http://code.google.com/p/darwincore/source/browse/trunk/xsd/profiles/germplasm/dwc_germplasm_0_1.xsd</a><br>
<a defaultcontextmenu="yes" href="http://rs.nordgen.org/dwc/germplasm/0.1/dwc_germplasm_0_1.xsd" target="_blank">http://rs.nordgen.org/dwc/germplasm/0.1/dwc_germplasm_0_1.xsd</a><br>
<br>
2. XML definition for IPT<br>
Listing the terms to use from the suggested DRAFT DarwinCore extension<br>
<a defaultcontextmenu="yes" href="http://rs.nordgen.org/dwc/germplasm/0.1/ipt_germplasm_0_1.xml" target="_blank">http://rs.nordgen.org/dwc/germplasm/0.1/ipt_germplasm_0_1.xml</a><br>
<br>
3. Add this XML definition to a copy of extensions.json<br>
Starting with: <a href="http://gbrds.gbif.org/registry/ipt/extensions.json">http://gbrds.gbif.org/registry/ipt/extensions.json<br>
</a>Add text {"title":"Germplasm","url":"<a href="http://rs.nordgen.org/dwc/germplasm/0.1/ipt_germplasm_0_1.xml">http://rs.nordgen.org/dwc/germplasm/0.1/ipt_germplasm_0_1.xml</a>","id":9}<br>
Saved as: <a href="http://rs.nordgen.org/rs/ipt/extensions.json">http://rs.nordgen.org/rs/ipt/extensions.json<br>
</a><br>
4. Modify ipt.properties<br>
PATH_TO_TOMCAT_WEBAPPS/ipt/WEB-INF/classes/ipt.properties<br>
Line 7: "registryUrl=<a href="http://gbrds.gbif.org/registry">http://gbrds.gbif.org/registry</a>" modified to<br>
"registryUrl=<a href="http://rs.nordgen.org/rs">http://rs.nordgen.org/rs</a>"<br>
<br>
5. Restart Tomcat (reload ipt)<br>
The new ipt.properties settings does not seem to be loaded without restart of tomcat<br>
<br>
6. Add/load the new extension to IPT<br>
Login with admin permissions<br>
<a defaultcontextmenu="yes" href="http://your_server_name/ipt/admin/extensions.html" target="_blank">http://your-ipt-service-url/ipt/admin/extensions.html</a><br>
Click "Check for all available extensions"<br>
Select the name of the new extension<br>
Select "install" and "Done"<br>
<br>
7. Mapping of terms to your data<br>
Select the new extension under "Add New Mapping"<br>
Click "Add" button to the right<br>
Select and map terms<br>
<br>
<span style="font-weight: bold;">Remarks:</span><br>
<br>
The IPT will contact the registry as defined in "ipt.properties". By 
default the GBIF registry in Copenhagen is defined here, but you may 
modify this to point to your own registry. I did not mimic the complete 
features of the registry - ONLY the list of extensions "extensions.json"
 to add the new draft germplasm extension I made. You may want to add 
your own thesaurus "thesauri.json" of controlled vocabulary or more 
features in the similar way. After loading my new extension to my IPT at
 NordGen, I modified the "properties.ipt" back to point to the GBIF 
registry in Copenhagen again.<br>
<br>
To mimic the registry feature for adding the extension, I made a copy of the file from <a href="http://gbrds.gbif.org/registry/ipt/extensions.json">http://gbrds.gbif.org/registry/ipt/extensions.json</a> and added my application schema from the extension as you will see at <a defaultcontextmenu="yes" href="http://rs.nordgen.org/rs/ipt/extensions.json" target="_blank">http://rs.nordgen.org/rs/ipt/extensions.json</a>.<br>
<br>
The application schema (as defined in "extensions.json") and online from: <a href="http://rs.nordgen.org/dwc/germplasm/0.1/ipt_germplasm_0_1.xml">http://rs.nordgen.org/dwc/germplasm/0.1/ipt_germplasm_0_1.xml</a>, creates a namespace (for the use by IPT) as well as includes the URL for the actual draft germplasm extension I made:<br>
<br>
http://rs.nordgen.org/dwc/germplasm/0.1/ http://rs.nordgen.org/rs/dwc/germplasm/0.1/dwc_germplasm_0_1.xsd<br>
<br>
The application schema itself (ipt_germplasm.xml) only lists the terms I
 want to use in IPT, with the property name to be displayed in the IPT 
mapping interface. To create this file I started with one of the other 
extensions <a href="http://gbrds.gbif.org/resources/extensions/vernacularName.xml">http://gbrds.gbif.org/resources/extensions/vernacularName.xml</a>.
 I just made a copy of this file and replaced the names and terms for 
vernacular name extension with the terms I wanted from the draft 
germplasm extension.<br>
<br>
<span style="font-weight: bold;">NB!</span> This DRAFT extension for 
germplasm is still under development and I am sure that I still 
duplicate some terms from DarwinCore or perhaps other extensions! I did 
not yet work much with the terms for trait observations on germplasm, 
but added most of the terms from the new proposed draft standard for 
these data for the European genebank community.
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<a class="post-count-link" href="http://dag-endresen.blogspot.com/2010_03_01_archive.html">March</a>
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<li><a href="http://dag-endresen.blogspot.com/2010/03/gbif-integrated-publishing-toolkit-ipt.html">GBIF Integrated Publishing Toolkit (IPT) installat...</a></li>
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<a class="post-count-link" href="http://dag-endresen.blogspot.com/2009_09_01_archive.html">September</a>
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